Utility of RNA Sequencing and Immunohistochemistry for NTRK Fusion in Thyroid Carcinoma

Neurotrophic tropomyosin receptor kinase (NTRK) fusion is one of the druggable driver genes of thyroid cancer, which is confirmed in surgical specimens. However, there is a risk that certain fusion patterns may not be detected using gene panel testing. This study aimed to identify patients harboring NTRK fusion who might be overlooked by panel testing.

Two patient groups were analyzed. Group A included patients with advanced thyroid cancer who underwent panel testing. Immunostaining for pan-tropomyosin receptor kinase (TRK) was performed, and RNA sequencing was added to cases without mitogen-activated protein kinase alterations. Group B, including surgical cases with papillary thyroid carcinoma, was screened by immunohistochemistry for BRAF mutation and pan-TRK. RNA sequencing was performed on BRAF-negative and pan-TRK-positive cases.

Among the 100 cases with advanced thyroid cancer in group A, gene panel testing detected mitogen-activated protein kinase alterations in 88. The most common alteration was the BRAF mutation (n=72), followed by RET fusion (8), RAS mutation (7), and NTRK fusion (1). Additional RNA sequencing for eight cases did not detect pathological NTRK fusions. Group B included 76 cases, in which immunostaining identified two cases with NTRK fusions: TFG-NTRK1 fusion was detected by panel testing, whereas SQSTM1-NTRK3 fusion was overlooked. In immunohistochemistry, NTRK1 fusion showed relatively strong staining, whereas NTRK3 showed weak staining. Notably, one case with the ETV6-NTRK3 fusion had no staining.

This study identified a case of thyroid carcinoma harboring NTRK fusion that was overlooked by panel testing. Active searching for NTRK fusions is desirable in cases without mitogen-activated protein kinase abnormalities or with pan-TRK staining.